modules/bracken_bracken

Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.

brackenmetagenomicsabundancekraken2

https://github.com/nf-core/modules/[...]/modules/nf-core/bracken/bracken

Description

Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`kraken_report`
`:file`

TSV file with six columns coming from kraken2 output

*.{tsv}

`database`
`:file`

Directory containing the kraken2/Bracken files for analysis

*

Output

name:type

description

pattern

`reports`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{tsv}

`bracken_report`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{tsv}

`txt`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.{tsv}

`bracken_kraken_style_report`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.txt

`versions_bracken`

`${task.process}`
`:string`

The process the versions were collected from

`bracken`
`:string`

The tool name

`bracken -v | cut -f2 -d"v"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`bracken`
`:string`

The tool name

`bracken -v | cut -f2 -d"v"`
`:eval`

The expression to obtain the version of the tool

Tools

bracken
GPL v3

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

ccb.jhu.edu/software/bracken ccb.jhu.edu/software/bracken/index.shtml?t=manual https://github.com/jenniferlu717/Bracken 10.7717/peerj-cs.104

modules/bracken_bracken

Description

Input

`meta`
`:map`

`kraken_report`
`:file`

`database`
`:file`

Output

`reports`

`meta`
`:map`

`bracken_report`
`:map`

`txt`

`meta`
`:map`

`bracken_kraken_style_report`
`:map`

`versions_bracken`

`${task.process}`
`:string`

`bracken`
`:string`

`bracken -v | cut -f2 -d"v"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`bracken`
`:string`

`bracken -v | cut -f2 -d"v"`
`:eval`

Tools

bracken
GPL v3

included in

maintainer

get in touch

modules/bracken_bracken

Description

Input

meta:map

kraken_report:file

database:file

Output

reports

meta:map

bracken_report:map

txt

meta:map

bracken_kraken_style_report:map

versions_bracken

${task.process}:string

bracken:string

bracken -v | cut -f2 -d"v":eval

Topics

versions

${task.process}:string

bracken:string

bracken -v | cut -f2 -d"v":eval

Tools

bracken GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`kraken_report`
`:file`

`database`
`:file`

`reports`

`meta`
`:map`

`bracken_report`
`:map`

`txt`

`meta`
`:map`

`bracken_kraken_style_report`
`:map`

`versions_bracken`

`${task.process}`
`:string`

`bracken`
`:string`

`bracken -v | cut -f2 -d"v"`
`:eval`

`versions`

`${task.process}`
`:string`

`bracken`
`:string`

`bracken -v | cut -f2 -d"v"`
`:eval`

bracken
GPL v3